[configuration] Move config sections into categories

SQL/9999-99-99-drop_tables.sql

@@ -93,6 +93,7 @@ DROP TABLE IF EXISTS `help`;
 DROP TABLE IF EXISTS `ConfigI18n`;
 DROP TABLE IF EXISTS `Config`;
 DROP TABLE IF EXISTS `ConfigSettings`;
+DROP TABLE IF EXISTS `ConfigCategories`;
 DROP TABLE IF EXISTS `menu_categories`;
 
 -- issues must be deleted before `modules` table

SQL/New_patches/2026-05-31_config-categories.sql

@@ -0,0 +1,36 @@
+CREATE TABLE `ConfigCategories` (
+    `ID` int(11) NOT NULL AUTO_INCREMENT,
+    `Name` varchar(255) NOT NULL,
+    `Description` varchar(255) DEFAULT NULL,
+    `Visible` tinyint(1) DEFAULT '0',
+    `Label` varchar(255) DEFAULT NULL,
+    `OrderNumber` int(11) DEFAULT NULL,
+    PRIMARY KEY (`ID`),
+    UNIQUE KEY `Name` (`Name`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+INSERT INTO ConfigCategories (Name, Description, Visible, Label, OrderNumber)
+SELECT Name, Description, Visible, Label, OrderNumber
+FROM ConfigSettings
+WHERE Parent IS NULL AND DataType IS NULL;
+
+ALTER TABLE ConfigSettings
+    ADD COLUMN CategoryID int(11) DEFAULT NULL AFTER Parent;
+
+UPDATE ConfigSettings child
+JOIN ConfigSettings category_setting ON child.Parent=category_setting.ID
+JOIN ConfigCategories category ON category.Name=category_setting.Name
+SET child.CategoryID=category.ID,
+    child.Parent=NULL
+WHERE category_setting.Parent IS NULL AND category_setting.DataType IS NULL;
+
+DELETE FROM ConfigSettings
+WHERE Parent IS NULL AND DataType IS NULL;
+
+ALTER TABLE ConfigSettings
+    ADD KEY `fk_ConfigSettings_CategoryID_idx` (`CategoryID`),
+    ADD CONSTRAINT `fk_ConfigSettings_CategoryID`
+        FOREIGN KEY (`CategoryID`)
+        REFERENCES `ConfigCategories` (`ID`)
+        ON DELETE SET NULL
+        ON UPDATE CASCADE;

modules/configuration/ajax/process.php

@@ -223,7 +223,6 @@ function getPathIDs(string $table): array
          */
         $query = "SELECT c.ID FROM Config c "
             . "LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) "
-            . "JOIN ConfigSettings csp ON (cs.Parent = csp.ID) "
             . "WHERE cs.DataType = 'web_path';";
         break;
     case 'ConfigSettings':
@@ -263,4 +262,3 @@ function validPath($value)
     }
     return true;
 }
-

modules/configuration/php/configuration.class.inc

@@ -108,8 +108,8 @@ class Configuration extends \NDB_Form
 
         $parentConfigItems = $DB->pselect(
             "SELECT Label, Name
-             FROM ConfigSettings
-             WHERE Parent IS NULL AND Visible=1 ORDER BY OrderNumber",
+             FROM ConfigCategories
+             WHERE Visible=1 ORDER BY OrderNumber",
             []
         );
 
@@ -129,6 +129,18 @@ class Configuration extends \NDB_Form
         $config = \NDB_Config::singleton();
         $DB     = $this->loris->getDatabaseConnection();
 
+        $categories = iterator_to_array(
+            $DB->pselect(
+                "SELECT ID, Name, Description, Visible, 0 AS AllowMultiple,
+                    NULL AS DataType, NULL AS Parent, Label, OrderNumber,
+                    0 AS Multilingual
+                 FROM ConfigCategories
+                 WHERE Visible=1
+                 ORDER BY OrderNumber",
+                []
+            )
+        );
+
         // Get the names and meta-information for the config settings in the database
         $configs = iterator_to_array(
             $DB->pselect(
@@ -143,18 +155,17 @@ class Configuration extends \NDB_Form
         foreach ($configs as &$setting) {
             try {
                 $setting['Disabled'] = 'Yes';
-                if ($setting['Parent'] != null) {
-                    $valueFromXML = $config->getSettingFromXML($setting['Name']);
-                    if (!is_array($valueFromXML)) {
-                        $setting['Value'][0] = $valueFromXML;
-                    } else {
-                        $setting['Value'] = $valueFromXML;
-                    }
+                $valueFromXML        = $config->getSettingFromXML($setting['Name']);
+                if (!is_array($valueFromXML)) {
+                    $setting['Value'][0] = $valueFromXML;
+                } else {
+                    $setting['Value'] = $valueFromXML;
                 }
             } catch (\ConfigurationException $e) {
                 $setting['Disabled'] = 'No';
             }
         }
+        unset($setting);
 
         // Now check for config settings from the database for the fields not
         // overridden in the config.xml
@@ -171,18 +182,37 @@ class Configuration extends \NDB_Form
                 }
             }
         }
+        unset($setting);
 
         // build a tree from configs array
-        $tree = [];
+        $settingsByID       = [];
+        $settingsByCategory = [];
         foreach ($configs as &$node) {
-            $node['Children']          = [];
-            $tree[intval($node['ID'])] = &$node;
+            $node['Children']                 = [];
+            $settingsByID[intval($node['ID'])] = &$node;
         }
+        unset($node);
+
         foreach ($configs as &$node) {
-            $tree[$node['Parent']]['Children'][] = &$node;
+            if ($node['Parent'] !== null) {
+                $settingsByID[intval($node['Parent'])]['Children'][] = &$node;
+                continue;
+            }
+
+            if ($node['CategoryID'] !== null) {
+                $settingsByCategory[intval($node['CategoryID'])][] = &$node;
+            }
+        }
+        unset($node);
+
+        foreach ($categories as &$category) {
+            $category['Disabled'] = 'No';
+            $category['Children'] = $settingsByCategory[intval($category['ID'])]
+                ?? [];
         }
+        unset($category);
 
-        return $configs;
+        return $categories;
     }
 
     /**

php/libraries/NDB_Config.class.inc

@@ -292,13 +292,27 @@ class NDB_Config
         if ($id === null) {
             $configSetting = $db->pselect(
                 "SELECT cs.ID as ParentID, child.ID as ChildID,
-                        cs.AllowMultiple, child.Name
+                        cs.AllowMultiple, child.Name, 0 AS IsCategory
                 FROM ConfigSettings cs
                     LEFT JOIN ConfigSettings child ON (child.Parent=cs.ID)
                 WHERE cs.Name=:nm",
                 ["nm" => $name]
             );
 
+            if (count($configSetting) === 0) {
+                $configSetting = $db->pselect(
+                    "SELECT cc.ID as ParentID, child.ID as ChildID,
+                            0 AS AllowMultiple, child.Name, 1 AS IsCategory
+                    FROM ConfigCategories cc
+                        LEFT JOIN ConfigSettings child ON (
+                            child.CategoryID=cc.ID
+                            AND child.Parent IS NULL
+                        )
+                    WHERE cc.Name=:nm",
+                    ["nm" => $name]
+                );
+            }
+
             if (count($configSetting) === 0) {
                 throw new ConfigurationException(
                     "Config setting $name does not exist in database"
@@ -307,26 +321,32 @@ class NDB_Config
         } else {
             $configSetting = $db->pselect(
                 "SELECT cs.ID as ParentID, child.ID as ChildID,
-                        cs.AllowMultiple, child.Name
+                        cs.AllowMultiple, child.Name, 0 AS IsCategory
                 FROM ConfigSettings cs
                     LEFT JOIN ConfigSettings child ON (child.Parent=cs.ID)
                 WHERE cs.ID=:nm",
                 ["nm" => $id]
             );
         }
 
+        $configSetting = array_values(iterator_to_array($configSetting));
+
         // If 1 row is returned, there are no children so we just want to
         // get the value from the database.
         // If multiple rows are returned, it means that there are children
         // for this element, so we need to build the tree to be consistent
         // with what would have come from the config.xml.
-        if (count($configSetting) === 1) {
+        $firstConfigSetting = $configSetting[0] ?? null;
+        if (count($configSetting) === 1
+            && $firstConfigSetting !== null
+            && $firstConfigSetting['ChildID'] === null
+            && intval($firstConfigSetting['IsCategory']) === 0
+        ) {
             // Trying to get a single value from the database.
-            $configSetting = $configSetting->getFirstRow();
-            if ($configSetting['AllowMultiple'] == '0') {
+            if ($firstConfigSetting['AllowMultiple'] == '0') {
                 $val = $db->pselectOne(
                     "SELECT Value FROM Config WHERE ConfigID=:CID",
-                    ['CID' => $configSetting['ParentID']]
+                    ['CID' => $firstConfigSetting['ParentID']]
                 );
                 if (empty($val)) {
                     return null;
@@ -337,18 +357,21 @@ class NDB_Config
                 // as ie. $config->getSetting("DoubleDataEntryInstruments")
                 $val = $db->pselect(
                     "SELECT Value FROM Config WHERE ConfigID=:CID",
-                    ['CID' => $configSetting['ParentID']]
+                    ['CID' => $firstConfigSetting['ParentID']]
                 );
                 $ret = [];
                 foreach ($val as $item) {
                     $ret[] = $item['Value'];
                 }
                 return $ret;
             }
-        } else if (count($configSetting) > 1) {
+        } else if (count($configSetting) >= 1) {
             // This was a parent element, so construct the children.
             $tree = [];
             foreach ($configSetting as $childSetting) {
+                if ($childSetting['ChildID'] === null) {
+                    continue;
+                }
                 $childName        = $childSetting['Name'];
                 $childID          = $childSetting['ChildID'];
                 $childValue       = $this->getSettingFromDB(
@@ -621,4 +644,3 @@ class NDB_Config
 
     }
 }
-

raisinbread/RB_files/RB_ConfigCategories.sql

@@ -0,0 +1,21 @@
+/*M!999999\- enable the sandbox mode */ 
+SET FOREIGN_KEY_CHECKS=0;
+TRUNCATE TABLE `ConfigCategories`;
+LOCK TABLES `ConfigCategories` WRITE;
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (1,'study','Settings related to details of the study',1,'Study',1);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (26,'paths','Specify directories where LORIS-related files are stored or created. Take care when editing these fields as changing them incorrectly can cause certain modules to lose functionality.',1,'Paths',2);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (39,'gui','Settings related to the overall display of LORIS',1,'GUI',3);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (43,'www','Web address settings',1,'WWW',4);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (45,'eeg_pipeline','EEG Pipeline settings',1,'EEG Pipeline',15);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (47,'dashboard','Settings that affect the appearance of the dashboard and its charts',1,'Dashboard',5);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (50,'imaging_modules','DICOM Archive and Imaging Browser settings',1,'Imaging Modules',6);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (57,'statistics','Statistics module settings',1,'Statistics',7);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (59,'mail','LORIS email settings for notifications sent to users',1,'Email',8);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (63,'uploads','Settings related to file uploading',1,'Uploads',9);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (65,'APIKeys','Specify any API keys required for LORIS',1,'API Keys',10);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (69,'imaging_pipeline','Imaging Pipeline settings',1,'Imaging Pipeline',14);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (111,'logs','Settings related to logging',1,'Log Settings',12);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (115,'minc2bids','Settings related to converting MINC to BIDS LORIS-MRI tool script',1,'MINC to BIDS Converter Tool Options',13);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (121,'aws','Settings related to AWS services',1,'AWS Settings',13);
+INSERT INTO `ConfigCategories` (`ID`, `Name`, `Description`, `Visible`, `Label`, `OrderNumber`) VALUES (135,'biobank','Settings related to the biobank module',1,'Biobank',14);
+UNLOCK TABLES;